Update usage docs

[drpatelh]

nf-core/nanoseq pull request

Many thanks for contributing to nf-core/nanoseq!

Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/nanoseq branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: CONTRIBUTING.md

[arontommi]

just one minor comment otherwise very good and understandable

[drpatelh]

Thanks @arontommi 👍 😎 Ive also updated the output docs so hopefully things are slightly clearer regarding the usage and output of the pipeline now...